Gone
by Hay389
Summary: How long has it been since she last counted? Oh, eighty two days now. Eighty two days since Supergirl, since her sister and best friend Kara, disappeared into thin air. Eighty two days since she went on a mission, and never came back.
1. Chapter 1

**Author's Note: So this is my first supergirl fan fiction. I had originally watched the show when it was on CBS, and started to watch it on the CW during the second season, but ended up not ****liking some changes so I dropped it. This past summer I got back into the show, and really enjoy it. I'm kind of happy I waited after the whole Mon-el situation, because I would have been even more pissed if I had watched it on air. I really did end up enjoying the pair. Anyways, I hope you like the story. I have two other stories I'm currently writing for for Supergirl as well. Also, I have no Beta, so sorry for any mistakes.**

**DISCLAIMER: I do not own Supergirl or any of its characters.**

* * *

2 and a half months, 11 and a half weeks, 81 days, 1944 hours, 116640 minutes, and 6998400 seconds. That's how long its been since Alex felt as if someone plunged their hand into her chest, tearing her heart out and squeezing just enough to make the pain radiate through her from head to toe, but not enough to kill her; not enough to put an end to the misery she had to swim in for the past, how long has it been since she last counted? Oh, eighty two days now.

Eighty two days since Supergirl, since her sister and best friend Kara, disappeared into thin air. Eighty two days since she went on a mission, and never came back.

It was supposed to be simple too, just survey an area where they thought a rogue alien was hiding out who had been causing trouble around the city. Alex suggested asking J'onn for assistance, but Kara smiled and shrugged her shoulders saying this was just like old times, nothing she hasn't done a million times by herself. That didn't exactly help ease her worry of Kara going somewhere alone, but she trusted her sister's judgement. After all, she always had contact with Kara—including the tracking device they put in her after she started working for the DEO.

She could hear Kara laugh as she flew to her destination, the wind blowing her cape and hair making her feel as carefree as always. Alex had smiled, her sister appreciates all the little things in life; the things most people are too busy to see.

Kara landed, and Alex could hear her breath hitch. She knew something wasn't right. "_Kara, what's wrong?"_

"_Alex, it's not—"_

That was all her sister got to say before her comm cut off, the tracking device being immediately deactivated. Alex wasted no time contacting J'onn for assistance, who was already rushing out the door when he heard something had happened to Kara. Alex met him at the factory, but it was exactly as it had been for years, abandoned. J'onn already searched the entire building, including the surrounding wooded area, but couldn't find any sign as to what happened to Kara. Alex didn't care though, she searched for hours again. Searched until J'onn threatened to fly her back home without her consent.

There really was nothing, though. There was no sign of anything that shouldn't have been in the abandoned factory, no fingerprints, no footprints, and no tire tracks. However, an agent had found a single syringe filled with Kryptonite on the last five minutes of the search thrown into a bush near the front of the woods. The only thing that told them though was Kara had been taken against her will.

Alex began tracking everything related to Kara. If someone even whispered Supergirl's name, she wanted to hear about it. With no real evidence to even know where to begin, Brainy suggested they try using a system where if Supergirl was mentioned anywhere, whether it be a phone call or text, the DEO would be alerted about it. Alex was willing to try anything, but after Brainy set everything up and alerts started coming in, Alex never realized just how much people text or tweet about Supergirl; bad and good stuff, nothing though that would look like the person might have an idea of where Kara is.

Alex even goes to the Alien Bar every night, keeping her ears out for anyone speaking about her sister. Nothing came of that either.

Eighty four days of living like that. It wasn't easy, but Alex couldn't give up on Kara. She knew her sister was out there somewhere. She would know, she would have this feeling of doom in the pit of her stomach if Kara was dead. Alex didn't even want to think of that possibility.

Alex sat upright, quickly jolted out of her sleep. Darkness still engulfed her apartment, so it was still night time. Had she gotten any sleep? She checked her phone which read 2:36 AM, August 25th. Today marked the eighty fifth day without her sister. Alex rubbed her eyes, laying back down, when she heard a loud bang at the door. That must have been what caused her to startle awake.

Sighing, she removed her covers and headed towards her front door not in the mood to socialize with anyone this early in the morning. You can say she was surprised to find Brainy on the other end. "Brainy? What are you doing here so early?" He gave her a look that made the tiredness she felt evaporate immediately.

"Yes, well this is urgent. I told you I would stay later to keep going through the texts and phone calls to see if anything popped out. Well, I found this." Brainy held up small futuristic device, displaying the tweet for Alex to read. "_It's funny, I thought life without Supergirl would be easier...more carefree. As I've sat here for the past two months of Supergirl's sudden disappearance, I realize that it's not Supergirl who has plagued this city, it's the technology we use. I've watched for years as the advancement of technology has destroyed families, not supergirl. I had listened to the Children Of Liberty, let them control me into thinking it was aliens that needed to be taken down. I realize my mistake now. Supergirl is not the enemy, is no longer the threat I thought her to be a few months ago, no alien is. It is the very phones we use that are. The people behind all the advancements, those people are the enemy. I know the truth, and soon everyone will too." _

"His name is Ronnie Walters."

Alex didn't need anymore convincing that this guy knew something about what happened to Kara. She threw on a coat and some shoes, not bothering to change out of her Pajamas. "Let's go."

"Right now?" Alex rolled her eyes. "I said let's go didn't I."

"I don't think going alone in the middle of the night is a good idea. You should wait for J'onn."

"I'm not waiting a few more hours for J'onn when we have a lead right now, and besides I'm not alone. You're coming too." Alex didn't leave room for any more argument as she grabbed her keys and walked out her door, Brainy following behind her.


	2. Chapter 2

**Author's Note: Hey everyone, I should have mentioned this before, but this story is set after the fourth season, but before the fifth. I got this idea, ****and**** then decided to use the trailer for season five and do my own thing. I don't want anyone to be confused going on. **

**Caroline1929: Yes! I also really enjoy the sister ****moments**** between Kara and Alex, it is honestly the main part of why I watch the show. I do plan on doing Kara's point of view, but not for a few chapters. **

**Thanks to everyone who left a review, I'm so happy to know you're enjoying the story. Let me know how you feel about this chapter!**

* * *

The loud cracking of the door being kicked in had startled the cat inside the house, hissing at Alex and Brainy as it padded right by them out the front door. It was black, and reminded Alex of Streaky—she remembered hearing Kara leave their room in the early mornings, months before school ended and long going into summer vacation, when Alex's curiosity finally won her over. After she heard the front door shut from downstairs, she threw on her soft brown boots and followed kara for a few blocks before her sister came to a halt. Kara reached her hand into her bookbag and pulled out a small cat food can, the snap of the top being peeled off attracting a kitten who was as black as the midnight sky. Kara had done that for months, watching as the small kitten turned into a grown cat, always watching it eat from the can she brought; but never did she pick up the friendly creature. Kara had been way too scared of hurting it as she was still trying to control her powers. Then one day when Alex had decided to follow Kara again, she watched as her sister opened a can but no cat came running. That went on for weeks before Kara realized Streaky was never coming back. She remembered consoling her sister the best she could, as things were still very awkward around them. "_Kara, It's fine. The cat probably just wandered off." _

"_No Alex, Streaky always comes. He hasn't been around for weeks." Alex watched as her sister cried on the couch, her hands trying to keep up with wiping away every tear that fell. Alex turned off the television, putting her hand over her sister's. "Kara, maybe he found another home."_

"_Why would he, he do that?" she hiccuped, her blue eyes finally staring up at Alex. "He might not have been able to keep living wherever he was, and he was forced to find a new home; kind of like you had to." Kara immediately understood after that, wrapping her arms around Alex. _Even though their relationship deteriorated immensely after that, as the family got the news Jeremiah had passed away, it was one of her earliest memories she had with Kara where they weren't fighting, but actually acting like normal sisters. Alex never told Kara how the day before Streaky disappeared that she found his body on the side of the road, a careless driver having run him over. She buried him for Kara, but didn't want to have to tell her about how her favorite thing had died. She thought it would have hit too close to home, literally, as the loss of her parents and entire planet was still fresh. Kara never stopped talking about that cat, even till this day. Whenever she mentions Streaky, a smile spreads across her face. That's how Alex knew keeping his death a secret was for the best.

"Cats. Useless creatures, aren't they?" Alex rolled her eyes at Brainy, as she stepped through the threshold of the front door. She flicked on the nearest light switch, but settled on her phone flashlight when no lights appeared. "Are you sure we have the right house Brainy?"

"I am 98.3 percent certain. This is the last known address of Ronnie Walters." Alex flashed her light over the living room, moving towards the kitchen. There was a single couch that sat in the center with a white sheet covering it, a layer of dust clearly visible on top. There was a bookshelf still overflowing with some collection, but hadn't been touched in a while. A few boxes were also spread out, but all they contained were more books—nothing suspicious. For the most part, the kitchen was in the same condition, bare, with no food in the fridge or in the cabinets, except for a few empty beer cans and water bottles spread out on the kitchen island.

She headed upstairs, the second to last step up making Alex flinch as a loud creak filled her ears, sounding close to nails on a chalkboard—something she always hated the sound of.

The hallway was surprisingly big, as four doors spread across it, two on each side. "I'll take the right, you take the left." Alex moved for the first, turning the golden handle and pushing the door open. It was just a bathroom, and just from standing at the opening she could tell that there wasn't going to be anything useful, but she checked under the sink and the small, almost closet like, dresser which held a few old towels still folded, but nothing; no item hidden within the towels either. She closed the bathroom door, noting the ladder that lead to the attic was now hanging down from the ceiling. "Brainy?"

"Up here."

"I'll be right up, I need to check the last room."

"Alex, you're going to want to see this." Alex glanced once more at her second door before climbing up the ladder, almost hitting her head on the way up. "What is it Brai—" she stopped midway her sentence, the view answering her question.

There were chains hanging from the wall inside a metal cage, ones where someone would have both their arms and feet chained up, and blood splattered everywhere. There wasn't one giant spot, but rather it looked like someone was injured and had been dragged or walked, blood dripping from whatever wound onto the light wooden floor. This would be awful to walk into period, but her eyes watered at the fact it could be Kara's blood. Alex gulped, having to know, "Brainy, what percentage do you have on that being Kara's blood?" Brainy just stared at the blood trail on the ground that stopped at the beginning of the ladder. "Brainy? Brainy!" Brainy flinched, his teary eyes meeting Alex's. "A 99.9 percent match."

Alex wiped at a tear that fell down her cheek. "Can...can you tell how old?" Brainy bent down to get a better look. "Two days. The blood isn't dark enough to have been more than a week. I am sorry, Alex."

Alex put her hands on her knees, bending down as if she were trying to catch her breath. They were so close to finding Kara, and yet she managed to slip between their fingers by a couple days. She should have looked harder, researched more; now her sister is somewhere god only knows, maybe not even in National City anymore, thanks to her carelessness. And if it couldn't get any worse, Kara was wounded. No, Kara could even be dead. It made her stomach flip, vomit threatening to come up. Her little sister was probably tortured for months, and her final moments could have been yesterday, wondering if her sister was even looking for her. With all the blood Alex can see, the idea suddenly becomes so much more realistic.

Kara is probably dead, and it's all her fault.

"Alex, I found this when I first got up here." Her head snapped up towards him, his hand outstretched with a syringe glowing green; it was almost empty, but with the drops left behind they could confirm it was definitely Kryptonite. "It is an identical match to the one found at the abandoned factory."

"So, she isn't…" she couldn't say dead out loud. If she did, it was almost confirming her thoughts. Brainy knew what she meant though. "Well, from this being left behind I would say no. For them to inject Kara with something to knock her out, whoever has her must of thought she was capable enough to escape at any given time; especially if they were transporting her from here, a suburban neighborhood. But...she is also injured, how badly I don't know."

"How much time do we have left to find her alive?" Brainy let a moment of silence pass. "With all this blood here, 24 hours, if she can hold on that long."

A loud creak interrupted the heavy air in the attic, making Alex look towards the ladder. It was the same sound that the step made when she stepped on it earlier; and she wouldn't have questioned it, but there wasn't anyone else in the house, and the cat had ran passed them outside when the pair had entered; that cat wouldn't have been heavy enough to make the stair creak anyway.

She listened hearing nothing at first, and then there was the sound of someone pounding down them as fast and hard as they could. Alex sprang into action, practically jumping down from the attic, and running down the stairs out the open front door.

To her left was Ronnie Walters sprinting as fast as he could. She started after him, following him into an alley on the street over, jumping a fence. He ran towards the back gate of the house that connected with the alley, but once he realized it was locked he took off down the left side of the house. Alex took the right side, coming out just a second before him. She tackled Ronnie to the ground. "Ronnie Walters, you are under arrest."

* * *

Alex called it in, the DEO coming within 10 minutes. She shoved Ronnie in the back of a car, having an agent wait with him as she wanted to personally bring him in herself. So far this was her only lead to Kara, and if he managed to escape then Kara might be gone for good. He knew something, and if the text didn't confirm it then all the blood in the attic of the house in his name did.

Alex met back up with Brainy in the attic, the forensic team searching for any evidence Brainy hadn't focused in on. They found a few strands of blonde hair in the cage, and traces of kryptonite. There were fingerprints, and of course all the blood—a sight that still made Alex sick, no matter how long she had time to process it was Kara's—but they couldn't confirm it to be Supergirl's until they got back to the lab.

Besides that, there wasn't anything else out of place. Alex was ready to get to the DEO and start interrogating her number one suspect, the sooner she found Kara the better; especially if she had less than 24 hours. She started to walk towards the exit, when the floorboard in the corner sticking up caught her attention. She didn't remember seeing that.

Alex easily removed it, and a few surrounding ones, until she pulled out a box. It was about as big as a shoebox, but she didn't recognize the brand's logo; and she's sure it probably won't matter. Removing the lid, she dropped the box, gasping. Inside was Kara's super suit, ripped up in many places, but almost completely stained in blood.


	3. Chapter 3

**Author's Note: ****Okay so this chapter is only Lena, but this is not going to be a fully Lena story. This story is mainly suppose to be the Danvers sisters; I just needed to fix the whole relationship with Lena and Kara, because we won't be getting that for a while on the show. This is also not a Supercorp fan fiction, sorry to break the news to anyone who likes them together. They are strictly best friends, that is it. Personally I wouldn't want to see the pair end up on the show, but I find I don't mind reading them together in certain fan fictions. Anyways, hope you enjoy this chapter!**

* * *

Lena felt as if she were a little girl again, when her mother and father would argue all the time over what seemed to her, everything. That had been in her early years when she first went to live with her father and she was too small to understand what exactly they were talking about, but smart enough to know whenever one of them said her name the argument was about her. Even then, as she got older, they kept arguing—being more discreet—until her father passed away. The huge mansion they lived in though could never filter out the noise of hearing her mother speak her name with so much resentment. Her past traumas, although are somewhat apart of the current problem, wasn't the main focus.

Because this time, it wasn't her parents fighting, it was her heart and brain.

Kara is Supergirl, had been the whole time, and never once did she try to tell her. Kara kept her in the dark, while everyone else around her knew her secret. She knew how much she hated when people in her life kept important things from her, how her life had been filled with lies. It was one of her insecurities, but Kara still kept the truth from her.

It all made sense too, the times where she would leave all of a sudden from Catco or cancel their lunch plans at the last second; it wasn't because Kara had gotten a very important lead, no, it was because Supergirl was needed somewhere in the city to save the day.

Lena really did love Kara, they were best friends after all, but maybe if she had told her two years ago, even three, Lena wouldn't have been as mad as she is. She probably would have been pissed, but wouldn't have felt as much anger and resentment as she does now.

Her brain was telling her she should be more than mad at her, she should inflict as much pain on Kara as the blonde had on her. Yet as shattered and torn as her heart is, she also felt that maybe Kara had a good reason not to tell her, after all she of all people should know what it's like to keep secrets—she is a Luthor. A part of her feels that she can't just throw away three years of friendship over the fact her friend didn't reveal her true identity to her, but that was before her and supergirl had ended up on bad terms. Kara sat there and purposefully put on an act with her, stood there and argued over the way she does things, when all along it was her best friend digging at her. A part of her wonders if that was how Kara felt the entire time; is it really Kara playing the part of Supergirl, or is it Supergirl playing the part of Kara?

Lena threw her pen across her desk, frustrated, knowing she wouldn't be getting any more work done in her current condition. Ever since Lex had shown her Supergirl's true identity, she couldn't really focus—and a part of that, all her anger, comes from the fact that she had to hear the big news from him of all people. How had her unstable brother managed to tell Lena the truth before Kara could?

She would only find all her answers from Kara, and she wished she could ask her questions, but that wasn't a possibility at the moment as the blonde is missing; has been for almost three months, and Lena would be lying if she said she didn't care. That is what has really been weighing on her mind these past few weeks, causing her to be behind on paperwork. The DEO has no clues as to who might have Kara, and She is sure Alex has been turning the city upside down looking for her sister; but as far as Lena knew, there was no new evidence since the initial search of the place Supergirl had disappeared.

Of course though, she didn't expect to be alerted of any new news anyway after what went down with Alex when she came to L-Corp looking for her help. That had been around the time Kara first went missing, and her feelings of betrayal and hatred were the only things keeping her grounded, as she felt as if she didn't feel anything then she would just float away. Alex marched in, and the more Lena thinks about it, she didn't look so good. She wondered how long they had been searching for Kara before resorting to asking for her help, as she's sure Alex knew by then that she had been ignoring Kara a full month before her sudden departure.

_Lena snapped her head up from her untouched paperwork, at the sudden sound of her office door hitting the wall—she wasn't even aware it could stretch that far back. It was Alex, and all the thoughts of thinking something urgent was happening with her company dwindled, anger replacing it. How dare Alex have the nerve to barge into her office unannounced, especially after three years of repetitive lies. "May I help you?" Her tone was cold, distant, and she knew it. Alex froze for a second, she knew Kara and Lena hadn't been talking, but what had she done to upset the Luthor? Whatever is was didn't matter, finding Kara did. _

"_I need your help Lena, Suprgirl is missing. She's been taken and we—"_

"_That's rich," Lena said, cutting Alex off. "You expect me to help with whatever problem your agency has run into, when you can't even be honest with the people you're working with."_

"_I don't know what you are talking about."_

"_I know. I know Kara is Supergirl."_

"_She told you? Is that why you ignored her for a whole month, because you didn't like she kept it from you? Kara was protecting you from—" _

"_I didn't need protection, I needed a friend. Someone who was honest with me and saw me for me, not a Luthor. Kara has been lying to me for three years about her true identity, even after I bared my soul out to her. I think I have the right to be pissed, especially after finding out from Lex of all people."_

"_Kara always planned on telling you, she just got caught up with saving National City. She was nervous to tell you because you were the only person who didn't know Kara was Supergirl, but still liked her anyway. Lena, she didn't want to lose that, lose you."_

"_And how am I supposed to believe that when the both of you have been lying to me since the Daxamite's invasion, even before then?"_

"_Look, I didn't come here to argue with you about your friendship with Kara, I need help to find her. She went missing during a mission and we have no leads, no evidence to know who to look at. I thought that maybe you'd—"_

"_I'd what, help? I'm sure she's fine, and that you'll be able to locate her without my resources."_

"_Lena, please. This is Kara, she hasn't done anything wrong here. She was just trying to protect you because once people find out her identity, they are exposed to her enemies. She'd rather know you're safe, then to have you know her identity and have your life be in jeopardy."_

"_I frankly don't care, Ms. Danvers. Now I'm going to kindly ask you to leave my office. Don't make me call security." Alex stared at Lena, not believing she wouldn't help find her best friend. "Fine, but if anything happens to her and you could've helped prevent it, I hope your anger over her life was worth it." Alex shut her door as hard as she came in, this time knocking her painting of the wall._

It took her a few days, but eventually the realization of Kara missing had sunk in. Eventually days turned into weeks, and the weeks turned into months—still no sign of supergirl. Her heart was starting to win the war, and she could no longer hide how worried she was for Kara. Lena no longer slept at night, she was lucky to get three or four hours at most. The bags under her eyes eventually set, followed by headaches and a cold—she had finally gotten over it about a week ago. She became a literal mess, and anyone around her could tell; especially James.

The month of her ignoring Kara, she had also ignored him because he knew who Supergirl really was. Really she ignored everyone who knew about Kara's secret. Then he reached out, and things were said, but they came to an understanding and are luckily still together. He could see though how much her missing friend was eating at her, because she could see it eating at him too; could see the same bags under his own eyes, the way he tossed and turned at night until he eventually got up from bed, resigned to his fate of getting no sleep. As hard as it was for her, James had been friends with Kara for a whole year before she entered the picture, and can only imagine how much he was feeling from her absence.

She could tell he wanted to help too, but being Guardian only got him so far before people would start to find out about his nightly runs, searching for any name or place that might lead to Kara. James even tried to convince her to rejoin the search for Supergirl, just explain to Alex what she told him, and she'll understand. Lena wanted to, but he hadn't heard the anger and hurt in Alex's voice when she marched into her office looking for help, just to be denied. Alex would just remind her that she didn't want to help when it was really needed, and that the DEO no longer requested her service, and was three months too late to say sorry.

Truth be told it wasn't Alex pushing her away that scared her, it was the fact that if Alex allowed her to help, what they would find if she managed to have a breakthrough on something the DEO has been stumped on for the past few months. Lena was terrified they would finally find Supergirl, and the gnawing feeling of worry would turn to dread, as they discover the kryptonian was no longer with them; her spirit vacant of this earth, an empty shell left behind.

If Kara was dead, how could Lena tell her that she forgave her for never telling her the truth of her true identity? That it took a few months to let Alex's words set in, but finally realized it was for her protection, even if she thinks she can handle everything on her own.

How were the pair ever going to have lunches together in her office, just the two of them, gossiping on the latest news out there? What about the exciting adventures they would go on from a lead Kara received for a story, insisting her best friend come along? Or gather at the blonde's loft for a game night, her and jimmy a pair, Kara and Alex, always fighting to be the winner; although she knew there was never a chance for victory with the way Alex and Kara knew each other, only having to nod to figure out what the other was saying. How was Lena supposed to move on, if Kara was lying six feet under; never again hearing her excitement over potstickers and pizza, or the goofy grin she got whenever Dorthy picked the apple off the tree just for it to be smacked out of her hand, stunned the tree could talk. It didn't seem fair for Lena to live a happy life without her best friend, if Kara left it thinking her best friend no longer wanted anything to do with her, hated her even.

Lena began to wonder if maybe her mother was right to have so much resentment towards her, because look how she had treated Kara; someone who was so full of hope and innocence. Maybe people had been right to question her intentions. Maybe she really was just a Luthor.


End file.
